Doubling the Cross-Linking Interface of a Rationally Designed Beta

Sep 16, 2014 - We have rationally engineered a stimulus-responsive cross-linking domain based on a repeats-in-toxin (RTX) peptide to enable ...
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Doubling the Cross-Linking Interface of a Rationally Designed Beta Roll Peptide for Calcium-Dependent Proteinaceous Hydrogel Formation Kevin Dooley, Beyza Bulutoglu, and Scott Banta* Department of Chemical Engineering, Columbia University, New York, New York 10027, United States S Supporting Information *

ABSTRACT: We have rationally engineered a stimulusresponsive cross-linking domain based on a repeats-in-toxin (RTX) peptide to enable calcium-dependent formation of supramolecular hydrogel networks. The peptide isolated from the RTX domain is intrinsically disordered in the absence of calcium. In calcium rich environments, the peptide binds Ca2+ ions and folds into a beta roll (β-roll) secondary structure composed to two parallel β-sheet faces. Previously, we mutated one of the faces to contain solvent exposed leucine side chains which are localized only in the calcium-bound β-roll conformation. We demonstrated the ability of this mutant peptide to self-assemble into hydrogels in the presence of calcium with the aid of additional peptide-based cross-linking moieties. Here, we have expanded this approach by engineering both β-roll faces to contain leucine residues, thereby doubling the crosslinking interface for each monomeric building block. These leucine rich surfaces impart a hydrophobic driving force for selfassembly. Extensive characterization was performed on this double-faced mutant to ensure the retention of calcium affinity and subsequent structural rearrangement similar to that of the wild type domain. We genetically fused an α-helical leucine zipper capable of forming tetrameric coiled-coil bundles to the peptide and the resulting chimeric protein self-assembles into a hydrogel only in calcium rich environments. Since this new mutant peptide enables cross-linking on both surfaces simultaneously, a higher oligomerization state was achieved. To further investigate the cross-linking capability, we constructed concatemers of the β-roll with maltose binding protein (MBP), a monomeric globular protein, without the leucine zipper domains. These concatemers show a similar sol−gel transition in response to calcium. Several biophysical techniques were used to probe the structural and mechanical properties of the mutant β-roll domain and the resulting supramolecular networks including circular dichroism, fluorescence resonance energy transfer, bis-ANS binding, and microrheology. These results demonstrate that the engineered βroll peptides can mediate calcium-dependent cross-linking for protein hydrogel formation without the need for any other crosslinking moieties.

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INTRODUCTION Protein-based biopolymer hydrogels composed of three-dimensionally cross-linked macroscopic networks have been widely investigated for a host of applications in the biomedical field because of their biocompatibility, predictable erosion rates, and tunable viscoelastic properties.1−5 Several excellent reviews are available that detail protein- and peptide-based self-assembly strategies.6−11 Biomolecules with the ability to respond “intelligently” to external stimuli such as pH, temperature, ionic strength, or light are often incorporated into monomeric polymer building blocks to trigger or disrupt self-assembly through a variety of mechanisms.12−14 Calmodulin, elastin-like polypeptides, and α-helical leucine zipper domains have been used to actuate hydrogel formation in response to environmental cues, leading to successful implementation into microfluidic systems, biosensors, and vehicles for controlled release.1,5,15−20 We have previously reported a rationally designed peptide based on the beta roll (β-roll) domain that functions as a © 2014 American Chemical Society

stimulus-responsive cross-linker for calcium dependent hydrogel formation.21 The β-roll scaffold was taken from the block V repeats-in-toxin (RTX) domain of adenylate cyclase from Bordetella pertussis.22 It is a modular, repeating polypeptide that undergoes a reversible structural rearrangement in response to calcium. The peptide is apparently intrinsically disordered in the absence of calcium and folds into a β-roll in calcium rich environments consisting of two parallel β-sheet faces separated by flexible turn regions (Figure 1a).22,23 Conserved aspartic acid residues in the turn regions are responsible for coordinating calcium ions. Only a C-terminal capping group is required for calcium-induced folding of the polypeptides.24,25 Each β-sheet face in the folded conformation contains eight residues with solvent exposed side chains that project radially away from the hydrophobic core. In our previous study, we Received: June 13, 2014 Revised: September 10, 2014 Published: September 16, 2014 3617

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Figure 1. Homology models for WT and mutant β-roll domains with primary sequences. Homology models for WTβ (a), Leuβ (b), and DLeuβ (c) domains were generated with SWISS-MODEL (Swiss Institute of Bioinformatics) using a β-roll-containing lipase as a template (PDB 2Z8X). Side and top-down views are given for each construct in the folded conformation with the red spheres representing bound calcium ions. The side chains of the surface exposed residues are highlighted and underlined in the primary sequences. The amino acids in magenta represent the wild-type residues, and the blue amino acids represent the rational leucine mutations. All images were rendered in PyMOL.

Figure 2. Monomeric polymer building blocks and assembled hydrogel networks. All cartoons represent β-roll domains in the folded conformation after calcium (red) binding. (a) HS-Leuβ monomer composed of an α-helical leucine zipper (yellow), a randomly coiled linker (purple), and the mutant Leuβ (light blue). The assembled network depicts an association number of 2 for Leuβ. (b) HS-DLeuβ monomer composed of an α-helix, linker, and DLeuβ mutant (green). Association numbers of >2 are depicted. (c) MBPDLeuβ-MBP-DLeuβ monomer. The DLeuβ can achieve higher oligomerization states and does not require cross-linking provided by the helical bundles. MBP is a monomeric protein and does not naturally self-assemble. α-Helices and MBP were rendered in PyMOL using PDB files 1GCL and 1YTV, respectively.

mutated one β-sheet face to contain leucine residues at these eight positions (Figure 1b). We fused the mutant leucine β-roll (Leuβ) to a self-assembling α-helical leucine zipper domain (H) and a randomly coiled hydrophilic linker (S) which is included to provide flexibility and prevent aggregation. Both H and S domains have been extensively characterized previously.26−28 Without calcium, the helices form tetrameric coiled-coil bundles, but the β-roll domains remain unstructured, delocalizing the leucine rich patches and prohibiting HS-Leuβ supramolecular self-assembly. After calcium binding, the β-roll folds and the leucine rich faces are exposed creating a hydrophobic driving force for oligomerization (Figure 2a). The resulting calcium-responsive hydrogel networks have been characterized using a variety of techniques.21 In this study, we have expanded this approach by further engineering the Leuβ peptide to increase its cross-linking capacity. The folded β-roll domain consists of two β-sheet faces, each with eight solvent exposed residues. We have now rationally engineered a “double-faced” leucine β-roll peptide (DLeuβ) such that all 16 positions are leucines (Figure 1c). This should enable cross-linking on both sides of the folded construct simultaneously, thereby increasing the potential oligomerization state and cross-linking density (Figure 2b). Previously, Leuβ domains were approximated to have an association number of 2 (Figure 2a), which required significant protein concentrations (60 mg/mL) and additional crosslinking moieties to assemble into supramolecular networks. We

hypothesize that DLeuβ will self-assemble at lower weight percentages as concentration dependent sol−gel transition and oligomerization state of the cross-linking domain are directly related.28 Further, DLeuβ should be able to induce calciumdependent self-assembly without the additional cross-linking provided by the α-helical leucine zippers. Circular dichroism (CD), fluorescence resonance energy transfer (FRET), and bisANS binding were used to ensure DLeuβ folds in a similar manner as the wild type β-roll (WTβ) and Leuβ in response to calcium. The mechanical properties of HS-DLeuβ were analyzed using a microrheology technique and compared to results obtained previously for HS-WTβ and HS-Leuβ.21 Finally, the utility of the DLeuβ as a stand-alone cross-linking domain was assessed by creating fusions to maltose binding protein (MBP) and analyzing the resulting hydrogel networks (Figure 2c).

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EXPERIMENTAL SECTION

Materials. Amylose resin, the MBP expression kit, and all enzymes for DNA cloning were purchased from New England Biolabs (Ipswich, MA). Isopropyl β-D-1-thiogalactopyranoside (IPTG) and ampicillin sodium salt were purchased from Gold Biotechnology (St. Louis, 3618

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MO). Amicon centrifugal filters were purchased from Millipore (Billerica, MA). All materials for polyacrylamide gel electrophoresis (PAGE) experiments as well as 1 μm Nile Red FluoSpheres for particle tracking were purchased from Life Technologies (Grand Island, NY). All oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA). BL21 Escherichia coli cells were purchased from Bioline (Taunton, MA). All other reagents were purchased from Sigma-Aldrich (St. Louis, MO) unless otherwise stated. Cloning into the pMAL Expression Plasmid. Cloning and expression of the WTβ and Leuβ constructs have been described previously.21 The DLeuβ peptide was assembled by annealing and extending two overlapping oligonucleotides encoding for the entire gene. The C-terminal cap of the β-roll domain was amplified from the pDLE-9-cyaA plasmid, a gift from Dr. Daniel Ladant (Institut Pasteur, Paris, France), and appended to the DLeuβ gene by overlap extension PCR.22 KpnI and HindIII restriction sites were added for ligation into a modified pMAL plasmid containing a self-cleaving intein, a gift from Dr. David Wood (Ohio State University, Columbus, OH).29 DLeuβ was also cloned into the same pMAL-Intein backbone modified with an α-helical domain (H) and a soluble linker (S) from the pQE9AC10Acys plasmid, a gift from Dr. David Tirrell (California Institute of Technology, Pasadena, CA).26 The resultant constructs, pMAL-Intein-DLeuβ and pMAL-Intein-HS-DLeuβ, were transformed into BL21 E. coli cells for expression. Concatemers of MBP and DLeuβ (Figure 2c) were cloned into the pMAL-c4e vector backbone. DLeuβ with the C-terminal cap was amplified out of the pMAL-Intein-DLeuβ construct and cloned using EcoRI and BamHI restriction sites. MBP was amplified from the pMAL-c4e construct and inserted after DLeuβ-Cap via BamHI and SalI restriction sites. Lastly, the second DLeuβ-Cap was amplified and cloned using SalI and HindIII restriction sites, resulting in the final construct: pMAL-MBP-DLeuβ-MBP-DLeuβ. During this cloning process, we also created the construct pMAL-MBP-DLeuβ to be used as a negative control. All oligonucleotide sequences for cloning experiments as well as primary sequences for all proteins can be found in the Supporting Information (Tables S3 and S4). Expression and Purification of DLeu Constructs. All DLeuβ constructs were expressed identically in Terrific Broth (TB) supplemented with 100 μg/mL ampicillin and 2 g/L D-glucose. Saturated 10 mL overnight cultures containing the appropriate transformed cells were diluted in 1 L of sterilized TB and grown at 37 °C and shaken at 220 rpm. Once the optical density (OD) at 600 nm reached 0.6, protein expression was induced with IPTG to a final concentration of 0.3 mM. Expression was carried out for either 5 h at 37 °C or 16 h at 25 °C, after which cells were harvested via centrifugation at 5000g for 10 min. Cell pellets were resuspended in 50 mL of MBP column buffer (20 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, pH 7.4) per liter of culture. Expressed protein was liberated from the cells by microtip sonication for 6 min on ice (Sonicator 3000, QSonica, Newtown, CT). Cell debris and insoluble protein were collected via centrifugation at 15 000g for 30 min and discarded. Soluble protein was diluted 5-fold in MBP column buffer and loaded onto equilibrated amylose resin drip columns. The columns were washed to remove any nonspecifically bound protein. MBP-DLeuβ and the concatemers were eluted with maltose and further purified on a Superdex HiLoad 16/60 size exclusion chromatography column (GE Healthcare). Columns containing proteins with the intein domain were saturated with intein cleaving buffer (137 mM NaCl, 2.7 mM KCl, 8.1 mM Na2HPO4, 1.76 mM KH2PO4, 40 mM bis-Tris, 2 mM EDTA, pH 6.2), capped, and incubated at 37 °C for 12−16 h. Cleaved fusion proteins were eluted with 50 mL of MBP column buffer and concentrated using either 10 or 30 kDa MWCO centrifugal filter devices. The samples were buffer exchanged into 20 mM bis-Tris, 25 mM NaCl, pH 6.0 and loaded onto a 16/10 Q FF ion exchange column (GE Healthcare). Target proteins were eluted using a linear NaCl gradient from 25 to 500 mM NaCl over 20 column volumes. Protein concentration was determined by absorbance at 280 nm using calculated extinction coefficients available in the Supporting Information (Table S1). Purified protein fractions were pooled and

concentrated, and buffer exchanged into the appropriate assay buffer. Purity and molecular weight for HS hydrogel forming constructs were confirmed by SDS-PAGE and MALDI-MS. These results are provided in the Supporting Information (Figure S1 and Table S2). Circular Dichroism Spectroscopy. β-Roll samples (100 μM) were loaded into a 0.1 mm path length quartz cuvette and analyzed on a J-815 CD spectrometer (Jasco, Easton, MD). The temperature was held constant at 25 °C via a Peltier junction temperature controller. Samples were incubated in the presence or absence of CaCl2 prior to analysis. All experiments were performed in triplicate in 50 mM Tris pH 7.4. Titration data were fit to the Hill equation using SigmaPlot (Systat Software, San Jose, CA) nonlinear regression software. Bis-ANS Dye Binding. β-Roll samples (1 μM) were prepared in 50 mM Tris pH 7.4 in the presence and absence of 50 mM CaCl2 prior to the addition of 5 μg/mL bis-ANS dye. Samples were loaded into a 1 cm path length UV cuvette and analyzed on a SpectraMax M2 cuvette reader (Molecular Devices, Sunnyvale, CA). Fluorescence emission was monitored from 420 to 600 nm following excitation at 390 nm. All measurements were performed in triplicate. Fluorescence Resonance Energy Transfer (FRET). β-Roll samples (1 μM) were prepared in 20 mM PIPES pH 6.8 supplemented with 120 mM NaCl and 10 mM KCl. A terbium(III) chloride stock solution was prepared in the same buffer. β-Roll samples were titrated with increasing amounts of terbium in 96-well microtiter plates and incubated at 25 °C for 30 min prior to analysis. Tyrosine residues in the β-roll domain were excited at 282 nm, and the fluorescence emission from bound terbium ions was monitored at 545 nm. All data were collected in triplicate. Hydrogel Preparation. All β-roll samples were prepared in a similar manner. Volumes of 500 μL of diluted protein samples were lyophilized in 5 mM Tris pH 7.4 supplemented with CaCl2 or MgCl2. Self-assembly was initiated by reconstituting the lyophilized protein in 1/10 the original volume, resulting in 4−6 wt % protein in 50 mM Tris pH 7.4. Mechanical mixing, vortexing, and centrifugation were used to ensure all of the lyophilized protein was rehydrated. Samples were allowed to set at room temperature for 30 min prior to analysis. Microrheology. Passive microrheology experiments were performed as previously described with minor modifications.21 When rehydrating lyophilized protein for particle tracking experiments, ddH2O was supplemented with 1 μm FluoSpheres conjugated with Nile Red. The samples were mixed, loaded onto a glass slide, and sealed with a coverslip. Particle motion was tracked using an Olympus IX81 motorized inverted microscope with a 40× objective. A highspeed Hamamatsu C9300 digital camera was used to record individual particle trajectories at an exposure time of 33 ms. For each run, 300 frames of video were recorded at 30 frames per second. Three runs were recorded per sample to ensure a good statistical average. All runs were recorded on a ThorLabs air table to eliminate ambient vibrational noise. All videos were analyzed using MetaMorph software and converted to TIFF stacks in ImageJ.30 Particle tracking and rheological analysis were completed in Interactive Data Language (IDL) software using algorithms created by Crocker et al.31−34 Mean square displacement (MSD) plots were generated and used to compare the mechanical properties of the prepared samples.

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RESULTS

DLeuβ Characterization. The rationally designed “doublefaced” leucine β-roll was expressed, purified, and characterized by CD, bis-ANS dye binding, and terbium binding assays to evaluate its response to calcium and self-assembly capability. We have previously characterized the WTβ and Leuβ using these same techniques.21 Samples (100 μM) of purified protein were analyzed by CD in the presence and absence of 10 mM CaCl2. The resulting spectra are shown in Figure 3a−c for WTβ, Leuβ, and DLeuβ constructs, respectively. All three proteins demonstrated similar conformational changes in response to calcium. In calcium-free environments, the spectra exhibited large negative peaks at 198 nm, which is indicative of 3619

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calcium rich samples, indicating a disordered to folded transition. Terbium, a fluorescent calcium analogue, was shown previously to trigger β-roll folding. 21,24 In the folded conformation, bound terbium ions are in close proximity to a tyrosine residue in the seventh repeat of the β-roll. Excitation of the tyrosine residue results in a fluorescence emission from the terbium ion proportional to the distance between the two.36 A terbium titration was performed while monitoring this fluorescence emission and the resulting plot is available in the Supporting Information (Figure S2a). While this does not directly report calcium-induced folding, it is consistent with the CD and bis-ANS data suggesting that the DLeuβ mutant retains its intrinsic stimulus-responsive conformational behavior. HS-DLeuβ Microrheology. An α-helical leucine zipper domain (H) and an unstructured hydrophilic linker (S) were appended to the N-terminus of the DLeuβ (Figure 2b). We previously demonstrated that this N-terminal fusion does not interfere with β-roll folding in response to calcium.21 Selfassembly into noncovalently cross-linked supramolecular networks was analyzed by passive microrheology. Time averaged MSDs of 1 μm fluorescent particles embedded into the samples were calculated over a range of lag times. The dynamics of the embedded particles report the mechanical properties of the surrounding microenvironment. In a purely viscous fluid, the tracer particles are allowed to freely diffuse and the MSD scales linearly with the lag time (τ). In an elastic medium, the MSD becomes independent of lag time and is characterized by a pronounced plateau over a sampled time domain.32,37,33 Initial experiments were conducted at 6 wt %, the concentration at which HS-Leuβ self-assembles in calcium rich environments. It should also be noted that 6 wt % HS-WTβ remained viscous regardless of the calcium concentration in our previous study.21 The results from the 6 wt % experiments are provided in Figure 4. HS-DLeuβ remained viscous in 50 mM MgCl2 at 6 wt % and assembled into an elastic network in the presence of 50 mM CaCl2 over the explored time domain (Figure 4a). An image of the assembled hydrogel is provided in Figure 4e. The rheology experiments were repeated at lower weight percentages to explore the lower critical protein concentration required for HS-DLeuβ self-assembly. The results at 4 wt % are shown in Figure 4b−d. Again, the HS-WTβ construct remained viscous in both magnesium and calcium rich solutions (Figure 4c). HS-Leuβ appeared largely viscous in both magnesium and calcium as well (Figure 4d). HS-DLeuβ remained viscous in magnesium and self-assembled into an elastic network over the sampled time domain in the presence of calcium (Figure 4b), similar to that observed at 6 wt %. To further explore the utility of the DLeuβ peptide and to take full advantage of the dynamic conformational response of the β-roll domain, we characterized the mechanical properties of 6 wt % HS-DLeuβ at varying calcium concentrations. Since self-assembly is mediated by β-roll folding, viscoelastic intermediate materials should be generated by using calcium concentrations in the dynamic range of β-roll folding. Figure 5 demonstrates the transition of 6 wt % HS-DLeuβ from largely viscous at low calcium concentrations to largely elastic at 10 mM calcium in the time range sampled. Interestingly, a viscoelastic intermediate was observed at 5 mM calcium. MBP-DLeuβ Concatemer Microrheology. In order to assess the utility of DLeuβ as a stand-alone cross-linking domain, we genetically constructed concatemers of DLeuβ and

Figure 3. β-Roll CD characterization. Mean residue ellipticity (MRE) plotted over a range of wavelengths for WTβ (a), Leuβ (b), and DLeuβ (c) in the presence (• • •) and absence () of 10 mM CaCl2. (d) Relative MRE at 218 nm for WTβ (●), Leuβ (△), and DLeuβ (◆) plotted over a range of calcium concentrations. All data were collected in triplicate in 50 mM Tris pH 7.4. Titration data were fit to the Hill equation using nonlinear regression software. The calcium binding parameters are summarized in Table 1.

randomly coiled peptide. Significant changes in secondary structure were observed in 10 mM CaCl2 for all β-roll domains. A random coil to β-sheet transition was evidenced by the emergence a negative peak at 218 nm and is consistent with previous reports.24 Slight variations in the CD spectra were most likely caused by small amounts of contamination in the samples from the recombination expression process. A titration was performed by monitoring the CD signal at 218 nm over a range of CaCl2 concentrations to elucidate the calcium binding parameters for each peptide (Figure 3d). The data were fit to the Hill equation, and the resulting parameters are summarized in Table 1. Leuβ and DLeuβ bound calcium with affinities Table 1. Calcium Binding Properties for WTβ, Leuβ, and DLeuβ Peptides construct

KD (mM)

nH

R2

WT Leu DLeu

0.91 ± 0.02 0.82 ± 0.01 1.18 ± 0.02

2.3 ± 0.1 3.1 ± 0.1 4.6 ± 0.3

0.997 0.998 0.998

similar to that of the wild type peptide, and all constructs exhibited cooperative binding with Hill coefficients (nH) > 1. Full CD spectra for all three constructs at all calcium concentrations tested are available in the Supporting Information (Figure S3). Bis-ANS is a commonly used molecular probe that binds to protein surfaces through hydrophobic interactions causing in an increase in fluorescence.35 It can be used to detect changes in protein structure and has been previously used to examine the structural transition of β-roll peptides in response to calcium binding.21,24 Purified DLeuβ was incubated with bis-ANS in the presence and absence of calcium, and the resulting emission spectra are available in the Supporting Information (Figure S2b). Significant increases in fluorescence were observed in the 3620

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of cross-linking content used in the 6 wt % HS-β-roll experiments. Rheological analysis was performed as described above and the results are provided in Figure 6a. A clear sol−gel

Figure 6. Time averaged MSD measurements for DLeuβ-MBP concatemers. Panel (a) provides MSD measurements for 21.3 wt % DLeuβ-MPB concatemers in the presence of 50 mM magnesium (○) and 50 mM calcium (●). The increased weight percentage was necessary to normalize the molar cross-linking content to the 6 wt % samples described previously. Panel (b) shows an identical experiment performed at 14.2 wt %, normalized to the molar cross-linking content of the 4 wt % samples described in Figure 4. Panel (c) shows an image of 21.3 wt % DLeuβ-MBP concatemer in the presence of 50 mM calcium suspended on a glass coverslip.

Figure 4. Time averaged MSD measurements for HS-β-roll constructs. 6 wt % (60 mg/mL) HS-DLeuβ MSD measurements in the presence of 50 mM magnesium (○) and 50 mM calcium (●) are given in panel (a). Identical experiments were performed at 4 wt % (40 mg/mL) for HS-DLeuβ (b), HS-WTβ (c), and HS-Leuβ (d). Only the HS-DLeuβ construct underwent a sol−gel transition in response to calcium at 4 wt %. Panel (e) shows an image of 6 wt % HS-DLeuβ in 50 mM CaCl2 suspended on a glass coverslip.

transition was observed in the presence of calcium, demonstrated by the lag time independence of the MSD, when compared to the magnesium control. A photograph of the cross-linked hydrogel suspended on a glass coverslip is provided in Figure 6c. Rheological analyses were also performed on samples with identical molar cross-linking content as the 4 wt % HS-β-roll experiments (14.2 wt %), and similar results were obtained. The MSD of samples prepared in the absence of calcium remained largely linear with respect to lag time while samples prepared in 50 mM calcium self-assembled into hydrogel networks in the time scales explored (Figure 6b). To supplement this data, the rheological properties of a truncated monomeric unit containing only one cross-linking domain (MBP-DLeuβ) were tested in the presence and absence of calcium at 21.3 and 14.2 wt %. As expected, these samples remained visually viscous, regardless of protein or calcium concentration, which is consistent with the MSD data provided in the Supporting Information (Figure S4).

Figure 5. Time averaged MSD measurements at various calcium concentrations for HS-DLeuβ. 6 wt % (60 mg/mL) HS-DLeuβ samples were prepared in increasing CaCl2 concentrations. MSD measurements in 0 mM (●), 0.5 mM (○), 1.0 mM (▼), 3.0 mM (△), 5.0 mM (■), and 10 mM (□) calcium are given. A transition from linear increases in MSD with respect to lag time in low calcium concentrations to a more pronounced plateau at higher calcium concentrations was observed.

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DISCUSSION In this work, we have rationally engineered a stimulusresponsive cross-linking peptide by exploiting the calcium induced conformational change intrinsic to the β-roll domain. The Leuβ and DLeuβ peptides require low millimolar concentrations of calcium to trigger self-assembly, which affords tight control over the gelation process. Additionally, viscoelastic properties can be allosterically regulated by simply adjusting the calcium concentration. Several biophysical techniques were used to investigate the structural responses of the mutant peptides to calcium, the lower critical protein

MBP. The monomeric block is shown in Figure 2c. In this case, the linkers are either composed of a poly asparagine linker at the C-terminus of MBP or the unstructured capping group at the C-terminus of DLeuβ. Primary sequences for all domains used in this work are provided in the Supporting Information (Table S3). Significantly higher weight percentages were required (21.3 wt %) to maintain the same molar concentration 3621

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providing a driving force for self-assembly. The viscosity of the medium increases causing a markedly slower growth rate of MSD vs τ and a pronounced plateau in the observable time range. In 50 mM CaCl2, we expect the β-roll domains to be fully folded thus localizing the leucine side chains into a structurally well-defined surface suitable for cross-linking. In our earlier work, the Leuβ peptide contained leucine residues on only one face of the folded β-helix which yielded a potential association number of 2 (Figure 2a).21 This required protein concentrations of 60 mg/mL (6 wt %) to induce selfassembly. At lower concentrations, there were not enough cross-links to sustain an elastic network. We hypothesized that by designing a β-roll peptide with cross-linking interfaces on both sides of the folded construct, the oligomerization state could potentially be increased (Figure 2b). Association numbers higher than 2 should facilitate self-assembly at lower protein concentrations. To investigate this, we prepared 40 mg/ mL (4 wt %) samples of HS-WTβ, HS-Leuβ, and HS-DLeuβ. Self-assembly was observed only for the HS-DLeuβ sample in calcium. All constructs remained viscous in the magnesium controls (Figure 4). HS-WTβ and HS-Leuβ MSD plots were indicative of a viscous medium in the presence of calcium as well. These rheological experiments suggest that DLeuβ has a higher association number than the Leuβ construct. At protein concentrations below 4 wt %, HS-DLeuβ assembled into several small elastic aggregates, but they did not constitute the entire volume, indicating fluctuations in local protein concentration (data not shown). We next investigated the potential of the DLeuβ cross-linking domain to allosterically regulate the mechanical properties of a 6 wt % gel. Samples were incubated in increasing concentrations of calcium, and the resultant MSD plots are provided in Figure 5. A clear transition was observed from a characteristically viscous medium at low calcium to an elastic medium at 10 mM calcium over the time domain sampled. The 5 mM calcium sample displayed characteristics of each limiting rheological behavior, that is, linear MSD growth with τ and limited fluctuation of MSD amplitude, particularly at small lag times. This is indicative of a viscoelastic intermediate in the given time scales.37 We have previously observed this phenomena with the HS-Leuβ construct, however, the transition from a viscous medium to a hydrogel occurred over a broader range of calcium concentrations.21 A strong correlation can be drawn between the calcium binding parameters of the two mutants and the allosteric regulation of the mechanical properties. The Leuβ peptide binds calcium cooperatively with a Hill coefficient of 3.1 as compared to 4.6 for DLeuβ. This means DLeuβ undergoes the structural transition from unfolded to folded over a more narrow range of calcium concentrations (Figure 3d), which is reflected in the sharp change in mechanical properties in Figure 5. The structural transition of Leuβ occurs over a broader range of calcium concentrations giving rise to a broader range of viscoelastic intermediates. These results further confirm our hypothesis that self-assembly is driven by β-roll folding. To further test the utility of the DLeuβ as a stimulus responsive cross-linking domain, we constructed concatemers of DLeuβ and MBP (Figure 2c), eliminating the α-helical leucine zipper domains. The microrheology results indicate similar calcium dependent self-assembly properties as seen with the HS constructs (Figure 6). Both 21.3 and 14.2 wt % samples in magnesium had significantly more viscoelastic character than the corresponding HS samples (Figure 6a,b). In order to

concentration required for self-assembly, and the mechanical properties of the resulting supramolecular networks. We have shown previously that mutating one face of the βroll peptide (Leuβ) has minimal impact on the affinity for calcium or the structural rearrangement induced upon calcium binding.21 By mutating both faces to contain leucine residues (DLeuβ), we have substantially increased the solvent exposed hydrophobic surface area of the folded construct. Despite the significant increase in hydrophobicity, no observable effects on protein solubility were detected for DLeuβ when compared to the other two constructs. Similar CD spectra were obtained in the presence and absence of 10 mM calcium for all three β-roll peptides indicating a disordered to β-sheet transition (Figure 3a−c). CD titration data were fit to the Hill equation, which assumes a two state binding model (disordered and folded) and multiple calcium binding sites. Fits from the titration data yielded similar affinities for calcium (∼1 mM); however, larger variations in the Hill coefficients, a measure of ligand binding cooperativity, were observed. Interestingly, both mutants bind calcium with a higher cooperativity than WTβ (Table 1); however, the relationship between solvent exposed hydrophobicity and Hill coefficient is not entirely clear. The data suggested that higher calcium concentrations were required to initiate folding, especially for the double mutant. The increased hydrophobicity of the DLeuβ may nonspecifically stabilize the peptide in the disordered conformation. Bis-ANS dye binding experiments were used to supplement the CD data and ensure the DLeuβ mutant retained the calcium binding properties intrinsic to the WTβ domain. Significant increases in fluorescence emission were detected in calcium rich solutions as compared to spectra obtained in the absence of calcium (Figure S2b). This increase in fluorescence can be attributed to an increase in hydrophobic surface area amenable to dye binding caused by calcium-induced folding. These results are in agreement with previously reported data for WTβ and Leuβ.21,24 Terbium binding assays were also conducted to further ensure the performance of the DLeuβ mutant (Figure S2a). Increases in fluorescence emission were observed with increasing terbium concentration, plateauing around 200 μM. Near identical hyperbolic responses were observed for WTβ and Leuβ.21 However, it is important to note that while terbium acts as a calcium analogue, it does not directly report calcium affinity. Taken together, the CD, bisANS, and terbium binding data suggest that all three constructs bind calcium in a similar manner resulting in a transition from a disordered state to a spatially organized β-roll structure. After the preliminary characterization was completed, the self-assembly capabilities of DLeuβ were assessed by two separate approaches. First we expanded our previous study by appending an α-helical leucine zipper domain (H) and a soluble linker (S) to the N-terminus of DLeuβ (Figure 2b). Microrheology experiments performed at 6 wt % confirmed HS-DLeuβ self-assembly into an elastic network in 50 mM CaCl2 while remaining a viscous liquid in 50 mM MgCl2 in the time domain explored (Figure 4a). These experiments verified what we have previously observed with Leuβ. In the absence of calcium, the data are consistent with a viscous solution, meaning the tracer particles can freely diffuse through the medium and ⟨r2(τ)⟩ increases linearly with τ. The helical domains can assemble into tetrameric coiled-coil bundles, but the unstructured β-roll domains prohibit the formation of an elastic network. In response to increasing calcium concentrations, the designed β-roll domains begin to fold, thus 3622

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normalize the molar cross-linking content between the HS and concatemer experiments, significantly higher protein concentrations were required due to the large size of MBP. However, a clear transition in mechanical properties was still observed for the concatemer samples at both weight percentages tested (Figure 6a,b). These results demonstrated that the DLeuβ mutant has the ability to create enough elastically effective associations to actuate self-assembly in the presence of calcium, without depending on additional cross-linking provided by the leucine zipper domains. A lower critical protein concentration for self-assembly was determined to be approximately 14 wt % (adjusted for molar cross-linking content), which is in agreement with the HS experiments discussed above (data not shown). The DLeuβ peptide is considerably different from other stimulus-responsive protein-associating domains used for hydrogel cross-linking. β-Roll domains do not naturally participate in self-assembly or biomolecular recognition; the self-assembly capabilities were rationally designed and engineered into the stimulus-responsive scaffold itself. More commonly, a naturally associating domain is placed in an environment which destabilizes the cross-linking interactions such as higher pH, temperature or by addition of denaturation agents. In contrast, the DLeuβ can be easily modulated from disordered to structured and, in turn, viscous to elastic by simply adjusting the calcium concentration. This may also offer a convenient strategy to encapsulate protein domains or cells inside a β-roll cross-linked hydrogel. Encapsulation targets can be incubated with soluble β-roll cross-linking domains after which calcium can be added to trigger macromolecular assembly, trapping protein or cells inside. Catalytically active proteins can also be genetically inserted in between β-roll crosslinking domains to create bifunctional stimulus responsive enzymatic hydrogels. Future experiments are planned to investigate erosion rates, reversibility of self-assembly and to further elucidate the mechanical properties of the β-roll hydrogels. While the microrheology experiments clearly demonstrate a sol−gel transition, the values of the storage and loss moduli have yet to be determined. Traditional oscillatory shear rheology over a larger time domain should provide more accurate measurements of the viscoelastic properties of these new materials.

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Article

ASSOCIATED CONTENT

S Supporting Information *

SDS-PAGE gels for hydrogel forming constructs. Terbium binding and bis-ANS binding experiments for DLeuβ. Full CD spectra for calcium titration for all three β-roll domains. Microrheology data for the MBP-DLeuβ fusion protein. Theoretical molecular weights and calculated extinction coefficients for all constructs. MALDI-MS results for HS constructs. Primary sequences for all constructs. Oligonucleotide sequences for all cloning experiments. This material is available free of charge via the Internet at http://pubs.acs.org

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Phone: 212-854-7531. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors gratefully acknowledge funding from the Air Force Office of Scientific Research (AFOSR) Grant Number FA955012-1-0112. The authors also thank Dr. Jennifer Haghpanah for her assistance with performing the MALDI-MS experiments.

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CONCLUSIONS

In this work, we have described a calcium responsive β-roll peptide with the ability to induce self-assembly into supramolecular networks. The β-roll scaffold was modified to create two hydrophobic surfaces suitable for cross-linking which are available only after calcium-induced structural rearrangement of the peptide. We have characterized the self-assembly capabilities of this domain by fusing an α-helical leucine zipper to the N-terminus and completing microrheology analysis. These chimeras were shown to self-assemble only in the presence of calcium. DLeuβ was also shown to self-assemble at lower protein concentrations than the single-faced mutant, indicating a higher association number. Furthermore, we have demonstrated the ability of the DLeuβ peptide to induce selfassembly without the additional cross-links provided by the leucine zipper by evaluating concatemers of DLeuβ and MBP. Thus, we showed that Dleuβ can serve as a new cross-linking domain, capable of hydrogel formation, which can be allosterically regulated via alteration of calcium concentrations. 3623

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